The AMPS package for multiple protein sequence alignment

AMPS (Alignment of Multiple Protein Sequences) is a set of programs for the multiple alignment of protein sequences. The programs build on the sequence comparison technique introduced in 1970 by Needleman and Wunsch (1). The Needleman and Wunsch algorithm when supplied with two protein sequences and a matrix of scores for matching each possible pair or amino acids (e.g., the identity matrix, or Dayhoff’s mutation data matrix [2]) calculates the best alignment between the two sequences and a score for the alignment. Although the Needleman and Wunsch algorithm may be used with virtually any pair of sequences, extending the method to more than three sequences is impractical even with today’s fast computers. In order to cope with the alignment of large families of protein sequences, a heuristic approach was therefore developed (3,4).